Integration of ATAC-seq and RNA-seq Unravels Chromatin Accessibility during Sex Reversal in Orange-Spotted Grouper (Epinephelus coioides)
Integration of ATAC-seq and RNA-seq Unravels Chromatin Accessibility during Sex Reversal in Orange-Spotted Grouper (Epinephelus coioides)
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ATAC-seq 和 RNA-seq 的整合揭示了橙斑石斑鱼 (Epinephelus coioides) 性逆转过程中染色质的可及性
DOI：
10.3390/ijms21082800
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发表时间：
2020-04
影响因子：
5.6
通讯作者：
Xiaochun Liu
中科院分区：
文献类型：
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作者：
Xi Wu;Yang;Chaoyue Zhong;Yin Guo;Tengyu Wei;Shuisheng Li;Haoran Lin;Xiaochun Liu
染色质结构在维持基因表达的精确调控中起着关键作用。染色质可及区是转录因子和顺式元件的结合部位。因此，来自这些开放区域的信息将加深我们对TF结合、染色质状态和基因表达调控之间关系的理解。我们采用转座酶可及染色质高通量测序技术(ATAC-SEQ)和RNA-SEQ分析方法对两性石斑鱼性反转过程中性腺中的染色质开放区域和TF结合部位进行了分析。我们重点研究了ZNF263、SPIB和KLF9等几个关键的转录因子，并分析了转录因子靶基因的网络。我们鉴定了许多转录本，在它们的目标基因中显示出性别偏好的表达，以及它们相关的开放染色质区域。然后，我们研究性相关基因的表达模式，以及在性逆转过程中某些基因的mRNA定位。我们发现了一组与性别相关的基因，经过进一步的研究，这些基因可能被确定为引发性别逆转的性别特异性或细胞特异性标记基因。此外，我们还发现了与性逆转相关的几个途径的核心基因(GNAS、ccnb2和cyp21a)，为进一步的研究提供了指南。
Chromatin structure plays a pivotal role in maintaining the precise regulation of gene expression. Accessible chromatin regions act as the binding sites of transcription factors (TFs) and cis-elements. Therefore, information from these open regions will enhance our understanding of the relationship between TF binding, chromatin status and the regulation of gene expression. We employed an assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq) and RNA-seq analyses in the gonads of protogynous hermaphroditic orange-spotted groupers during sex reversal to profile open chromatin regions and TF binding sites. We focused on several crucial TFs, including ZNF263, SPIB, and KLF9, and analyzed the networks of TF-target genes. We identified numerous transcripts exhibiting sex-preferred expression among their target genes, along with their associated open chromatin regions. We then investigated the expression patterns of sex-related genes as well as the mRNA localization of certain genes during sex reversal. We found a set of sex-related genes that—upon further study—might be identified as the sex-specific or cell-specific marker genes that trigger sex reversal. Moreover, we discovered the core genes (gnas, ccnb2, and cyp21a) of several pathways related to sex reversal that provide the guideposts for future study.
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影响因子：
30.8
作者：
He, Housheng Hansen;Meyer, Clifford A.;Shin, Hyunjin;Bailey, Shannon T.;Wei, Gang;Wang, Qianben;Zhang, Yong;Xu, Kexin;Ni, Min;Lupien, Mathieu;Mieczkowski, Piotr;Lieb, Jason D.;Zhao, Keji;Brown, Myles;Liu, X. Shirley
通讯作者：
Liu, X. Shirley
甲基睾酮摄食和甲基睾酮戒断引起的雌性橙斑石斑鱼性别变化的分子调控
影响因子：
3.6
作者：
Wang Qing;Liu Yun;Peng Cheng;Wang Xiang;Xiao Ling;Wang Dengdong;Chen Jiaxing;Zhang Haifa;Zhao Huihong;Li Shuisheng;Zhang Yong;Lin Haoran
通讯作者：
Lin Haoran
影响因子：
4.1
作者：
Xia, Wei;Zhou, Li;Gui, Han-Fang
通讯作者：
Gui, Han-Fang
DOI：
10.1016/s1532-0456(03)00136-4
发表时间：
2003-07
期刊：
Comparative biochemistry and physiology. Toxicology & pharmacology : CBP
影响因子：
--
作者：
Shinn‐Lih Yeh;C. Kuo;Y. Ting;Ching-Fong Chang
通讯作者：
Shinn‐Lih Yeh;C. Kuo;Y. Ting;Ching-Fong Chang
影响因子：
--
作者：
Q. Lu;B. Richardson
通讯作者：
Q. Lu;B. Richardson